cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta --interval_padding 100 -i 869_XA6-N1-BDNA-1_A23FG3YLT4_1.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo TNhaplotyper2 --tumor_sample 869_XA6-N1-BDNA-1_A23FG3YLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon.hotspot_protected.raw.vcf.gz 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.vcf.gz --algo OrientationBias --tumor_sample 869_XA6-N1-BDNA-1_A23FG3YLT4_1 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.orientation_data.tsv --algo ContaminationModel --tumor_sample 869_XA6-N1-BDNA-1_A23FG3YLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.segments 869_XA6-N1-BDNA-1_A23FG3YLT4_1.tnseq_tumor_only.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113726318, elapsed 10.8s, est remaining 205.4s, peak mem 703MB, user 110.1s, sys 2.0s, output queue size 46
progress 10% @chr2:3778716, elapsed 24.7s, est remaining 222.2s, peak mem 829MB, user 231.6s, sys 3.9s, output queue size 450
progress 15% @chr2:178609108, elapsed 38.7s, est remaining 219.1s, peak mem 829MB, user 357.6s, sys 6.5s, output queue size 12
progress 20% @chr3:57503916, elapsed 53.0s, est remaining 212.0s, peak mem 832MB, user 498.7s, sys 8.2s, output queue size 54
progress 25% @chr4:70768438, elapsed 66.8s, est remaining 200.3s, peak mem 846MB, user 620.5s, sys 9.9s, output queue size 298
progress 30% @chr5:132642070, elapsed 76.4s, est remaining 178.3s, peak mem 851MB, user 713.2s, sys 11.9s, output queue size 275
progress 35% @chr6:105373269, elapsed 100.6s, est remaining 186.8s, peak mem 888MB, user 940.0s, sys 13.9s, output queue size 559
progress 40% @chr7:107618228, elapsed 118.9s, est remaining 178.3s, peak mem 895MB, user 1090.7s, sys 15.6s, output queue size 582
progress 45% @chr8:143824213, elapsed 136.7s, est remaining 167.1s, peak mem 921MB, user 1256.1s, sys 17.5s, output queue size 14
progress 50% @chr10:21759070, elapsed 152.0s, est remaining 152.0s, peak mem 921MB, user 1396.0s, sys 19.1s, output queue size 25
progress 55% @chr11:34142175, elapsed 168.3s, est remaining 137.7s, peak mem 944MB, user 1532.7s, sys 20.6s, output queue size 187
progress 60% @chr12:14640982, elapsed 184.9s, est remaining 123.3s, peak mem 944MB, user 1680.0s, sys 22.1s, output queue size 176
progress 65% @chr13:32235978, elapsed 199.0s, est remaining 107.2s, peak mem 944MB, user 1805.3s, sys 23.7s, output queue size 384
progress 70% @chr15:37941571, elapsed 210.8s, est remaining 90.4s, peak mem 959MB, user 1918.5s, sys 25.2s, output queue size 302
progress 75% @chr16:28062976, elapsed 226.9s, est remaining 75.6s, peak mem 1007MB, user 2078.5s, sys 26.8s, output queue size 139
progress 80% @chr17:40089106, elapsed 243.3s, est remaining 60.8s, peak mem 1007MB, user 2241.2s, sys 29.0s, output queue size 153
progress 85% @chr19:1652201, elapsed 263.3s, est remaining 46.5s, peak mem 1007MB, user 2436.1s, sys 31.4s, output queue size 36
progress 90% @chr19:54666594, elapsed 286.0s, est remaining 31.8s, peak mem 1007MB, user 2640.1s, sys 33.7s, output queue size 16
progress 95% @chr22:32151387, elapsed 302.1s, est remaining 15.9s, peak mem 1019MB, user 2802.3s, sys 35.8s, output queue size 68
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 321.3s, est remaining 0.0s, peak mem 1019MB, user 2983.2s, sys 38.4s, output queue size 7
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 23311410395
output file size: 3209417
reads: 300045579
contig: 178193 intervals 76355618 bases
"assemble": 20947 calls 150.464 user 0.601 sys 153.614 real
"assemble_addRead": 20947 calls 3.912 user 0.008 sys 4.169 real
"assemble_buildGraph": 46704 calls 69.347 user 0.162 sys 70.812 real
"assemble_computecigar": 30253 calls 8.400 user 0.049 sys 8.597 real
"assemble_kg_build_calcsize": 46704 calls 37.467 user 0.094 sys 38.419 real
"assemble_kg_build_clear": 62447 calls 6.505 user 0.016 sys 6.602 real
"assemble_kg_build_prepare": 93408 calls 41.697 user 0.226 sys 42.482 real
"assemble_kg_build_threading": 30961 calls 28.758 user 0.028 sys 29.351 real
"assemble_kg_op1": 30961 calls 18.283 user 0.094 sys 18.442 real
"assemble_kg_op2": 30961 calls 0.613 user 0.000 sys 0.538 real
"assemble_kg_op3": 30961 calls 0.652 user 0.030 sys 0.652 real
"assemble_sg_clean": 30253 calls 2.569 user 0.018 sys 2.841 real
"assemble_sg_create": 30253 calls 4.288 user 0.017 sys 4.428 real
"checkGraph": 20947 calls 0.042 user 0.000 sys 0.071 real
"findHaplotype": 20947 calls 9.108 user 0.063 sys 9.358 real
advance: 189104 calls 983.743 user 16.719 sys 995.353 real
assemble_region: 20947 calls 163.725 user 0.671 sys 167.483 real
build_pileup: 186604 calls 8.571 user 0.048 sys 8.833 real
build_stats: 187335 calls 268.497 user 1.401 sys 281.074 real
build_variants: 17165 calls 0.103 user 0.000 sys 0.133 real
calc: 364018 calls 143.713 user 0.466 sys 156.480 real
calc_region: 17165 calls 747.165 user 1.564 sys 776.353 real
call_region: 17165 calls 15.232 user 0.025 sys 16.363 real
clip_region: 38112 calls 15.188 user 0.007 sys 15.880 real
done: 1 calls 20.521 user 0.115 sys 20.639 real
execute: 1 calls 0.000 user 0.006 sys 321.295 real
fetch: 743546 calls 275.317 user 1.149 sys 284.748 real
fetch_ref: 766452 calls 25.595 user 1.299 sys 6.295 real
fetch_region: 20947 calls 5.255 user 0.022 sys 5.387 real
fetch_vcf: 189104 calls 54.558 user 1.592 sys 61.708 real
idle: 275 calls 0.015 user 0.007 sys 253.410 real
init: 1 calls 0.058 user 0.000 sys 0.060 real
pairhmm: 179559 calls 1328.551 user 2.295 sys 1337.920 real
realign: 17165 calls 141.412 user 0.339 sys 160.868 real
region: 367297 calls 923.409 user 2.375 sys 956.733 real
tracker: 367297 calls 1.126 user 0.040 sys 1.493 real
trim_region: 20947 calls 0.284 user 0.000 sys 0.288 real
overall: 1216065536 mem 3815.073 user 43.490 sys 342.768 real